DNA – Interactive Angents

Phạm Thu Trang: 21001842

Phan Trần Thảo Vy: 21001850

I. INTRODUCTION

1. Basis for DNA – Interactive Drugs

An receptor with which drugs can interact is deoxyribonucleic acid (DNA) - the
polynucleotide that carries the genetic information in cells. Drugs that interact with this
receptor (DNA-interactive drugs) are generally very toxic to normal cells. Therefore, these
drugs are reserved only for life - threatening diseases such as cancers and microbial
infections.
One feature of cancer cells that differentiates them from that of most normal cells is that
cancer cells undergo a rapid, abnormal, and uncontrolled cell division. Because these cells
are continually undergoing mitosis, there is a constant need for rapid production of DNA
(and its precursors). However, because of rapid cell division, cancer cell mitosis can be
halted preferentially to that found in normal cells where there is sufficient time for the
triggering of repair mechanisms
DNA damage in a cell is sensed by several as yet poorly defined mechanisms involving a
number of proteins, especially p53. Activation of p53 in response to DNA damage in
normal cells can result in several other possible cellular responses, including upregulation
of DNA repair systems, cell cycle arrest (to allow time for DNA repair to occur), or
programmed cell death (apoptosis). Tumor cells, however, are defective in their ability to
undergo cell cycle arrest or apoptosis in response to DNA damage. Cancer cells that cannot
undergo cell cycle arrest are thus more sensitive to DNA-damaging agents. Because DNA
is constantly being damaged, which leads to 80–90% of human cancers, these DNA lesions
must be excised, generally by DNA repair enzymes.
This is not a chapter on antitumor agents, but rather on the organic chemistry of DNA
interactive drugs and the ways in which DNA damage relates to cancer chemotherapy.
2. Toxicity of DNA – Interactive Drugs
The toxicity associated with cancer drugs usually is observed in those parts of the body
where rapid cell division normally occurs, such as in the bone marrow, the gastrointestinal
(GI) tract, the mucosa, and the hair.
The clinical effectiveness of a cancer drug requires that it generally be administered at
doses in the toxic range so that it kills tumor cells but allows enough normal cells in the
critical tissues, such as the bone marrow and GI tract, to survive, thereby allowing recovery
to be possible.
Even though cancer drugs are very cytotoxic, they must be administered repeatedly over a
relatively long period of time to be assured that all of the malignant cells have been
eradicated. According to the fractional cell kill hypothesis, a given drug concentration that
is applied for a defined time period will kill a constant fraction of the cell population,
independent of the absolute number of cells. Therefore, each cycle of treatment will kill a
specific fraction of the remaining cells, and the effectiveness of the treatment is a direct
function of the dose of the drug administered and the frequency of repetition. Furthermore,
it is now known that single-drug treatments are only partially effective and produce
responses of short duration. When complete remission is obtained with these drugs, it is
only short lived, and relapse is associated with resistance to the original drug.
3. Combination Chemotherapy
The improved effectiveness of combination chemotherapy compared to single-agent
treatment is derived from a variety of reasons: initial resistance to any single agent is
frequent; initially responsive tumors rapidly acquire resistance after drug administration;
anticancer drugs themselves increase the rate of mutation of cells into resistant forms;
multiple drugs having different mechanisms of action allow independent cell killing by
each agent; cells resistant to one drug may be sensitive to anothert.
4. Drugs Interactions
The most significant problem associated with the use of combination chemotherapy is drug
interactions; overlapping toxicities are of primary concern.
5. Drug Resistance
As indicated earlier, the prime reason for the utilization of combination chemotherapy is to
avoid drug resistance. Suffice it to say here that tumor cells, like microbial cells, have
multiple possible mechanisms for counteracting the effects of drugs, including mutating
the drug target, excluding a drug from entering or staying in the cell, and mechanisms for
destroying the drug once it enters the cell
II. DNA STRUCTURE AND PROPERTIES

1. Basis for the Structure of DNA

 DNA Structure

The four deoxyribonucleotides containing the two purine bases—adenine (A) and guanine
(G)—and the two pyrimidine bases—cytosine (C) and thymine (T)—are linked by bonds
joining the 5′-phosphate group of one nucleotide to a 3′-hydroxyl group on the sugar of the
adjacent nucleotide to form 3′,5′-phosphodiester linkages

2. Base Tautomerization
A change in the tautomeric form would have disastrous consequences with regard to
hydrogen bonding because groups that are hydrogen bond donors in one tautomeric form
become hydrogen bond acceptors in another form, and protons are moved to different
positions on the heterocyclic ring

It has now become clear that hydrogen bonding is not the only factor that controls the
specificity of base pairing; shape may also play a key role. Kool has synthesized several
nonpolar nucleoside isosteres that lack hydrogen bonding functionality to determine the
importance of hydrogen bonding for DNA. When substituted in a DNA in which it is
paired opposite to adenine, it adopts a structure identical to that of a T–A base pair.The
benzimidazole isostere of deoxyadenosine is less perfect in shape but is still a good
adenosine mimic in DNAs. When 6.4 was incorporated into a template strand of DNA,
common polymerases could selectively insert adenosine opposite it, and the efficiency was
similar to that of a natural base pair. This suggests that Watson–Crick hydrogen bonds are
not necessary to replicate a base pair with high efficiency and selectivity and that steric and
geometric factors may be at least as important in the polymerase active site.The nucleoside
triphosphate derivative of 6.4 was made, and it was shown to insert selectively opposite to
an A in the template strand.Isostere 6.5 also was a substrate for polymerases, and a pair
between 6.4 and6.5 also was replicated well. The most important property of bases for
successful base pairing may be that they fit as snugly into the tight, rigid active site of
DNA polymerase
as would a normal base pair, and, therefore, complementarity of size and shape may as
important as its hydrogen bond ability

3. DNA Shapes
How is it possible for such a large quantity of DNA to be crammed into each nucleus of a
cell, given that the nucleus is only 5μm in diameter? It is accomplished by the packaging of
DNA into chromatin.
Some DNA is single stranded or triple stranded (triplex), but mostly it is in the double-
stranded (duplex) form. Some DNA molecules are linear and others (in bacteria) are
circular (known as plasmids). Linear DNA can freely rotate until the ends become
covalently linked to form circular DNA; then, the absolute number of times the DNA
chains twist about each other (called the linkage number) cannot change. To accommodate
further changes in the number of base pairs per turn of the duplex DNA, the circular DNA
must twist, like when a rubber band is twisted, into supercoiled DNA (Figure 6.8).
There are two general types of topoisomerases into which at least six different
topoisomerases have been classified; these topoisomerases regulate the state of
supercoiling of intracellular DNA:
- DNA topoisomerase I: removing positive and negative supercoils by catalyzing a
transient break of one strand of duplex DNA and allowing the unbroken,
complementary strand to pass through the enzyme-linked strand, thereby resulting in
DNA relaxation by one positive turn.
- DNA topoisomerase II: catalyzing the transient breakage of both strands of the duplex
DNA, with a 4 bp stagger between the nicks. This generates a gate through which
another region of DNA can be passed prior to religating (reattaching) the strands.
Therefore the outcome of this process is the supercoiling ofthe DNA in the negative
direction or relaxation of positively supercoiled DNA, which changes the linkage number
by negative two. The type I enzymes are further classified into type IA, type IB, or type IC
subfamilies
Scheme 6.1 shows general mechanisms for topoisomerase IA and IB. A tyrosyl group on
the enzymes attacks the phosphodiester bond of DNA, giving one of the two possible
covalent adducts, known as cleavable complexes, depending upon whether the enzyme is
in subfamily type IA (Scheme 6.1, pathway a) or type IB (Scheme 6.1, pathway b).

4. DNA Conformation
There are three general helical conformations of DNA: A-DNA, B-DNA, and Z-DNA.
Each conformation involves a helix made up of two antiparallel polynucleotide strands
with the bases paired through Watson–Crick hydrogen bonding, but the overall shapes of
the helices are quite different.

A-DNA and B-DNA differ in the distance required to make a complete helical turn (called
the pitch), in the way their sugar groups are bent or puckered, in the angle of tilt that the
base pairs make with the helical axis, and in the dimensions of the grooves. Whereas there
are 11 nucleotides in one helical turn in A-DNA, there are only 10 bp/pitch in B-DNA.
Therefore, A-DNA is shorter and squatter than B-DNA.
Z-DNA, a minor component of the DNA of a cell, is a left-handed double helix having
12bp per helical turn. In Z-DNA, the glycosyl bond connecting the base to the deoxyribose
group is oriented anti at the pyrimidine residues but syn at the purine residues (6.7). This
suggested that transient regions of Z-DNA, generated by transcription or unwrapping of
DNA, form in our chromosomes and may play a role in virus pathogenesis and gene
expression.
III. CLASSES OF DRUGS THAT INTERACT WITH DNA
There are three major classes of clinically important DNA-interactive drugs:
- Reversible binders: interact with DNA through the reversible formation of noncovalent
interactions;
- Alkylators: react covalently with DNA bases
- DNA strand breakers: generate reactive radicals that produce cleavage of the
polynucleotide strands.